Beacham et al.: Population identification of Oncorhynchus tshawytscha by variation at microsatellite loci 



245 



British Columbia (Dempson et al.**) (Fig. 1). The test fishery 

 is conducted from April to October annually and operates 

 daily (two sets of 30-min duration are made consecutively) 

 except during commercial gillnet fishery openings. In 

 1995, a single mesh size of 20.3 cm (8.0 inch) was used to 

 capture chinook salmon, and samples were collected from 

 all chinook salmon caught in the fishery and surveyed for 

 variation at five microsatellite loci. Further details of the 

 test fishery have been outlined by Shubert et al. (1988). 

 During 1997-99, operculum punches preserved in 90% 

 ethanol were obtained from commercial fisheries in the 

 lower Fraser River and mid Fraser. We were also able to 

 obtain operculum punches from chinook salmon caught in 

 marine fisheries in British Columbia that had previously 

 been marked with coded-wire tags (CWTs) and for which 

 the CWT had been recovered and decoded to determine 

 marking location. We subsequently used this sample of 

 83 Fraser River fish to evaluate the accuracy of estimated 

 stock compositions using a sample of known origin. 



Conversion of allele sizes between manual and 

 automated sizing systems 



In the 1998 and subsequent fishery samples, we surveyed 

 variation at OtslOO. OtslOl, Otsl02, Otsl04. Otsl07. and 



^ Dempson, J. B., J. R. Irvine, and R. E. Bailey 1998. Relative 

 abundance and migration timing of chinook salmon iOncorhyn- 

 chus tshawytscha) from the Fraser River. British Columbia, 

 Albion test fisherv, 1981-1995. Can. Man. Rep. Fish. Aquat. 

 Sci. 2459, 25 p. 



Ssal97 on the automated sequencer. However, estimated 

 allele sizes at these loci differed between those derived 

 from nondenaturing gels stained with ethidium bromide 

 and those derived from the denaturing gels and flourescent 

 tags on the automated sequencer. In order to convert allele 

 sizes between the two systems, we analyzed approximately 

 600 fish on both systems and determined the distributions 

 of allele frequencies. By inspection of the allele frequencies, 

 we were able to match specific allele sizes obtained from 

 the sequencer to specific allele sizes from the manual gels, 

 and then convert the sizing in the automated sequencer 

 data set to match that obtained from the manual gels. 

 Estimated allele sizes from both systems were very highly 

 correlated (r2>0.987 for all loci). In general, sizes for the 

 same allele from the sequencer were larger than those 

 estimated from manual gels, with the differential increas- 

 ing with allele size. 



Population structure 



Regional structure was observed in the baseline popula- 

 tions; the Birkenhead River, the lower Fraser River, mid 

 Fraser River, upper Fraser River, lower Thompson River, 

 North Thompson River, and South Thompson River popu- 

 lations comprised seven geographically based groups or 

 "stocks" (Beacham et al., 2003). The populations surveyed 

 in each of these regions are summarized in Table 1. 



Identification of individuals 



Identification of individuals to specific populations was 

 done with the program GENECLASS 1.0 (Cornuet et al., 



